[gmx-users] domain decomposition and load balancing

Amit Choubey kgp.amit at gmail.com
Sat Feb 20 00:10:06 CET 2010

Hi Mark,

I dont think i need to play with npme at all.


On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey <kgp.amit at gmail.com> wrote:

> Hi Mark,
> I am not using PME calculation.
> I was hoping mdrun will do the cell allocation itself.
> Thanks,
> Amit
> On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
>> ----- Original Message -----
>> From: Amit Choubey <kgp.amit at gmail.com>
>> Date: Saturday, February 20, 2010 8:51
>> Subject: [gmx-users] domain decomposition and load balancing
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > Hi Everyone,
>> > I am trying to run a simulation with the option "pbc=xy" turned on. I am
>> using 64 processors for the simulation. The mdrun_mpi evokes the following
>> error message before starting the md steps
>> >
>> > There is no domain decomposition for 64 nodes that is compatible with
>> the given box and a minimum cell size of 0.889862 nm> Change the number of
>> nodes or mdrun option -rdd or -dds>
>> Look in the log file for details on the domain decomposition>
>> > This has to do with the load balancing in the domain decomposition
>> version of mdrun. Can anyone suggest me how to set the option -rdd or -dds?
>> Those options are not normally the problem - but see the log file for info
>> and mdrun -h for instructions.
>> You should read up in the manual about domain decomposition, and see about
>> choosing npme such that 64-npme is a number that is suitably composite that
>> you can make a reasonably compact 3D grid so that the minimum cell size is
>> not a constraint. Cells have to be large enough that all nonbonded
>> interactions can be resolved in consultation with at most nearest-neighbour
>> cells (and some other constraints).
>> I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45
>> gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the
>> cells to have the smallest diameter possible. Of course if your simulation
>> box is so small that the 2D DD for pbc=xy will always lead to slabs that are
>> too small in one dimension then you can't solve this problem with DD.
>> If pbc=xy permits a 3D DD, then the same considerations apply. npme=19
>> gives 5x3x3 but npme=28 allows 4x3x3
>> > Also the simulation runs fine on one node (with domain decomposition)
>> and with particle decomposition but both of them extremely slow.>
>> Well, that's normal...
>> Mark
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